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Defuse Fusion Discovery With Gzipped Fastq Input

Hi,

I am running out of space on my server and wish to have deFuse software running with gzipped fastq input files. Previously, I decompressed them, expanding them sometimes 4-fold. There is no way for me to erase other things on the server. I have tried to follow the manual and setting the data_converter_1 in the configuration file but to no avail. Is there a more elegant way of doing this than decompressing and then at the end of the deFuse run, delete the decompressed files?

If I only had single reads, I could have done something to the effect of:

zcat input.fastq.gz | perl defuse.pl -c config.txt -

but I have pair-ended reads.

Anyone got suggestions? Thanks in advance.

fastq
• 3,656 views • link
updated by Sean Davis Sean Davis • written by ndejay • ndejay

2 answers

Untested, but in bash (and probably others), you can often use process substitution which avoids having to explicitly make FIFOs.

perl defuse.pl -c config.txt -1 <( zcat input1.fastq.gz ) -2 <( zcat input2.fastq.gz )
• 186 views • link
written by Sean Davis Sean Davis

Will both substituted processes run in parallel or serially?

• 0 views • link
written by ndejay • ndejay

They will run in parallel and will "stream" so that the entire file is not read into memory.

• 227 views • link
written by Sean Davis Sean Davis

You can always create named pipes:

mkfifo file1
mkfifo file2
zcat input1.fastq.gz > file1 &
zcat input2.fastq.gz > file2 &
perl defuse.pl -c config.txt -1 file1 -2 file2 ...

In general, something like that will work. Remember to delete the FIFOs when you're finished.

• 150 views • link
written by Devon Ryan Devon Ryan

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